1H0Y

Structure of Alba: an archaeal chromatin protein modulated by acetylation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of Alba: An Archaeal Chromatin Protein Modulated by Acetylation

Wardleworth, B.N.Russell, R.J.M.Bell, S.D.Taylor, G.L.White, M.F.

(2002) EMBO J 21: 4654

  • DOI: 10.1093/emboj/cdf465
  • Primary Citation of Related Structures:  
    1H0X, 1H0Y

  • PubMed Abstract: 
  • Eukaryotic DNA is packaged into nucleosomes that regulate the accessibility of the genome to replication, transcription and repair factors. Chromatin accessibility is controlled by histone modifications including acetylation and methylation. Archaea possess eukary otic-like machineries for DNA replication, transcription and information processing ...

    Eukaryotic DNA is packaged into nucleosomes that regulate the accessibility of the genome to replication, transcription and repair factors. Chromatin accessibility is controlled by histone modifications including acetylation and methylation. Archaea possess eukary otic-like machineries for DNA replication, transcription and information processing. The conserved archaeal DNA binding protein Alba (formerly Sso10b) interacts with the silencing protein Sir2, which regulates Alba's DNA binding affinity by deacetylation of a lysine residue. We present the crystal structure of Alba from Sulfolobus solfataricus at 2.6 A resolution (PDB code 1h0x). The fold is reminiscent of the N-terminal DNA binding domain of DNase I and the C-terminal domain of initiation factor IF3. The Alba dimer has two extended beta-hairpins flanking a central body containing the acetylated lysine, Lys16, suggesting three main points of contact with the DNA. Fluorescence, calorimetry and electrophoresis data suggest a final binding stoichiometry of approximately 5 bp DNA per Alba dimer. We present a model for the Alba-DNA interaction consistent with the available structural, biophysical and electron microscopy data.


    Related Citations: 
    • The Interaction of Alba, a Conserved Archaeal Chromatin Protein, with Sir2 and its Regulation by Acetylation
      Bell, S.D., Botting, C.H., Wardleworth, B.N., Jackson, S.P., White, M.F.
      (2002) Science 296: 148
    • Preliminary Crystallographic Studies of the Double-Stranded DNA Binding Protein Sso10B from Sulfolobus Solfataricus
      Wardleworth, B.N., Russell, R.J.M., White, M.F., Taylor, G.L.
      (2001) Acta Crystallogr D Biol Crystallogr 57: 1893

    Organizational Affiliation

    Centre for Biomolecular Science, St Andrews University, North Haugh, St Andrews, Fife KY16 9ST, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA BINDING PROTEIN SSO10BA100Saccharolobus solfataricusMutation(s): 0 
UniProt
Find proteins for P60849 (Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2))
Explore P60849 
Go to UniProtKB:  P60849
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60849
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.251 
  • R-Value Observed: 0.251 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.68α = 90
b = 84.68β = 90
c = 87.14γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-09-05
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance